Evangelion: Illustrious Thesis
by Fyrstorm
Summary: When Yui Ikari is swallowed up by Unit-01, Shinji is sent off by his father- but not to his teacher, or his aunt and uncle. No, Shinji is taken in by his godmother; Mari Makinami, one of his mother's old colleagues who lives in England. With a brand new family, things turn out... different. But how far gone is the Scenario, and what will happen when the mysterious Angels appear?
1. Rekindling and Extinguishing

**_Evangelion: Illustrious Thesis_**

 _Chapter One: Rekindling and Extinguishing_

.

Beautiful. He was beautiful.

Yui Ikari gazed down at the tiny boy swaddled in her arms.

"Shinji."

Her son looked back at her, eyes wide with the sort of inquisitive awe that only someone as young as he would have, and blinked. Yui sighed with contentment, softening from the warmth inside her. Finally pulling her eyes away from the boy, the woman turned to look up at her husband, sitting on the other side of the room from her. Gendo smiled back, with the same stilted awkwardness his expressions always had.

"He's wonderful," the man said. "You're wonderful."

.

Yes, everything was good for the little family, even as the world outside mended itself from the recent calamity. The times were changing, and little Shinji would find himself with a great role to play.

But across the seas was someone else destined to play a part in deciding this new world's fate...

.

* * *

\- _Saintford University, England_

 _Rrrrrring! Rrrrrring! Rrrrrri-_

A hand slapped down on the phone, fumbling for a solid grip. Lifting it up, the very tired woman attached to it sighed, and accepted the call. There were bags under her blue-green eyes, her hair was a tangled mess, and the apartment smelled of sweat, tea, and the faintest hint of lemon, but there was no reason she couldn't _still_ manage to be punctual.

 _~Probably someone else down in the labs.~_

"Makinami here," the young lady said breathlessly. "What is it now?"

 _"_ _Hello, Mari-san."_

Mari's breath caught in her throat. A swarm of emotions and memories rose up, chaotic and uncertain.

"Y-Yui?"

On the other end of the line, Mari's old acquaintance _giggled_.

 _"_ _It's been a long time, hasn't it?"_

"I… yes, it has," the young woman replied, forcing off the tension that had built up. "What are you calling for, Yui?"

 _"_ _I have some wonderful news to share with you, Mari,"_ she answered. Mari nodded.

"Yeah?" the scientist asked, resisting the urge to get off the bed and stand up. "What is it?"

 _"_ _I have a son."_

And just with those four words, Mari found herself almost completely speechless- for the second time that day. All the sleeplessness and physical exhaustion of the last week seemed to weigh down on her in one instant. It was a good thing she'd been lying down for this.

"You… you have a son," the nineteen-year old repeated. Another giggle.

 _"_ _His name is Shinji,"_ Yui added. This time, Mari managed to avoid _completely_ parroting her ex-colleague's words as the impact sunk in.

"Shinji… Yui, is there anything else you were calling for?" Mari asked slowly. Call her paranoid, cautious, or whatever- while the news was fantastic, she still expected there to be something else.

 _"_ _...Yes,"_ the woman replied. _"Mari-san, I want you to be his godmother."_

"...W-wait, what?"

 _"_ _If anything happens to me or Gendo in the future, I want_ you _to be able to take care of him,"_ Yui continued. _"Please, Mari."_

The young woman sighed. Her emotional relationship with Yui was still very confusing for her, even after three years- and this really wasn't helping her.

What should she do? Should she accept? Refuse? Did she even have a _reason_ to refuse at this time?

.

… No, she supposed she didn't.

"...As you wish, Yui-san," Mari sighed. She could do this. She could be a godmother to Yui's newborn.

After all, it wasn't like anything was going to happen to Yui.

Right?

.

* * *

.

 _"_ _No!"_ Mari cried, slamming her fist into the table. The burst of passion fizzled away, replaced with the heavy weight of mourning.

"D-dammit, no..." the woman sobbed, the news playing over and over in her head like a horrible chant.

Yui was gone. She was never coming back.

It had been some accident- Mari didn't know the details. All she'd gotten was that Yui had tried something new, some sort of experiment, and it had gone horribly, awfully wrong.

She was gone. She was never coming back.

Mari's emotions had always been in a sort of flux when it came to Yui, up until now. Now, she was no longer conflicted- just heartbroken.

.

But, as expected, the world didn't stop its turning for her.

 _Rrrrrring! Rrrrrring! Rrrrrring!_

Drawn by the tone, the woman turned, trying to smother her grief for the moment. Wearily, she picked up the phone, and accepted the call.

"Y-yes? This… this is Makinami."

 _"_ _Take Shinji."_

The voice was harsh, a pang of loneliness bleeding through behind it.

"G-Gendo?" Mari asked cautiously.

 _"_ _Just… take Shinji,"_ the man repeated. _"I… I can't-"_

The call cut off, leaving the woman to herself, alone and confused.

.

 _~"Take Shinji"... "If anything happens to me or Gendo in the future"... I guess he's all that's left.~_

Mari slumped forwards, wiping the tears from her eyes. She could do this. She could be strong. She… she could…

Her breath caught again, coming out as a ragged shudder.

 _She's dead, dead, dead, DEAD,_ _ **DE-**_

Mari bit down on her tongue, the pain cutting off the surge of despair before it could overwhelm her.

"D-dammit, Mari," she muttered to herself, pushing herself up. "Keep it together." The young woman looked across her apartment, eyes settling on one of the few photos she had around here; a teenaged girl and two young women, all very happy. The picture was dated 1998; the year she'd first met Yui Ikari.

Mari swallowed, and clenched her fists.

.

"Guess… guess I'll be going back to Japan for a bit, then," she said, to nobody in particular.

"Wish me luck."

* * *

It was a few days later that Mari managed to get there. The address itself was easy enough- Yui had sent her a couple letters before, so Mari had an easy way to figure out where to go.

What she _wasn't_ expecting was to meet her new ward quite a distance away from his actual house.

Mari had recently exited the train, and walked out towards the exit, when her attention was caught by the sound of… crying? Yes, crying- the same sort of broken sobbing that the woman herself had done before, just a while earlier. Mari stopped- and looked around, searching for the source of the sound.

...and there he was; a little boy about three or four years old, huddled up on a bench by himself. Mari's brow furrowed, and her hand snuck into her pocket, digging around. The woman drew out her wallet, and flipped it open, looking through the few pictures she'd brought. A quick comparison of the boy to the photos… and that confirmed it.

The woman walked over, slowly making her way to the other side of the bench. The boy didn't notice, until Mari finally sat down- and even then, he only glanced at her for a second, his sobbing dying down.

.

"H-hey there."

"..."

"Um…" Mari scratched her head. "Are you Shinji?"

"..."

"Come on, you can trust me. I was one of your mom's friends."

Finally, Shinji- for he _was_ Shinji- responded, giving a little nod. Mari smiled back softly.

"There we go. I'm Mari, Mari Makinami. I'm here to… to take care of you."

The boy blinked, a little confused.

 _~Of course,~_ Mari thought to herself. _~He's just a kid, they wouldn't have explained it to him.~_

"O-okay, so, here's how it works," she explained slowly. "I'm… I'm your godmother. That means that if your mom… if your mom and dad can't take care of you, then I will. Even got a card to prove it. Does that make sense?"

Another nod from Shinji.

"Good," the woman sighed. A little bit of sitting in silence would be just fine with her for now.

.

"...Say, kid," she asked. "Do you know where your dad is?"

Shinji shook his head.

"Left me here," he mumbled. Mari perked up.

"He… he _left you_ here? Alone?"

The boy looked around, slightly worried, and nodded. Mari grimaced.

 _~Gendo just_ left him _here, only a few days after… after that? But why would…~_

Mari brushed that thought away. She'd need a while before actually she could properly focus on that. But in the meantime… she had a kid with no mom, and a dad who'd just handed him off to her. Mari was by no means a parent, but that didn't mean she couldn't _try_ \- for Yui's sake, and the kid's sake, at least.

"...say," she began. Shinji looked over towards her. Mari shuffled a little bit closer. "How about this; I promise that _I_ won't leave you, okay?"

"...Do you mean it?"

Mari's gaze softened.

"Shinji, if I told you I didn't mean it, I'd be hurting myself just as much as you."

"Huh?"

"Of _course_ I mean it."

* * *

\- _Ten years later._

.

"...'Come'," Mari read, unamused at the letter before her. "It just says 'come'? _Really?_ "

Her godson shrugged.

"I guess. I mean, it's… _dad_ ," the fourteen-year old replied. "Fatherly love and compassion wasn't his strong suit." He glanced down at the paper, and sighed. "Even so… maybe I should go, just to see what he wants."

The woman looked at him.

"You _really_ want to?" she asked.

"I… I don't think it could hurt much," Shinji said. Mari rubbed the back of her head.

"...Alright then, I won't stop you," she said. " _But_ , I'm going with you."

"Hm?"

Mari adjusted her glasses, and fixed her godson with a slight smirk.

"I said I'll be going with you, Shinji. There's _no_ way in hell that I'm letting your father fuck things up _again_ \- especially not after _last time_."

.

There was a moment of pause, as the message sank into the boy's psyche. Then, spontaneously, Shinji rushed forwards, and embraced the woman, pulling himself tight against her.

"Thanks for everything, mom."

That oh-so-familiar warmth tugged at Mari's heartstrings again. She reached down, and wrapped her arms around him.

"Of course, Shinji."


	2. Transit and Remembrance

**_Evangelion: Illustrious Thesis_**

 _Chapter Two: Transit and Remembrance_

.

Ultimately, they had decided to go and see what Gendo wanted. Mari, as she'd promised, had accompanied her godson on the trip- and she'd admit, she _was_ curious just why his father had called for him, especially after abandoning the boy to her care. So, the day after the letter, they'd packed up a couple of suitcases, purchased two tickets, and taken a plane to Japan. Quick and easy.

Mari had to be honest; this was only the fourth time she'd crossed between England and Japan, and cross-continental travel… wasn't really her thing. The woman never did very well with jet lag, and long journeys like this tended to bring out the worst of it. However, that wasn't going to stop her from keeping Shinji company- not even a little.

In an attempt to negate the worst of it, Mari had chosen to just get some shut-eye during the flight.

Of course, the thing about sleep is that it brings dream- dreams of the future, the present… and the past.

And dream, Mari did.

.

* * *

It wasn't easy for her, being a mom.

Mari had more than a few sleepless nights and tired days before she got a few of her mates from work- namely, those who also had kids- to start helping her out. Even then, it was still difficult. She'd had to remember all manner of new things; pack Shinji's lunches, attend school meetings when you need to, don't stay at work too late because Shinji didn't have the keys to the front door and you actually have to pick him up… overall, it was _definitely_ more stressful and confusing than she had anticipated. A couple of times- back in the early days of it- she'd even found herself startled at the fact that the boy was _there_ at all.

.

But with time came experience, and nothing _truly_ awful ended up happening to Shinji because of her issues. As the years passed, the whole "parent" thing started to become closer to a second nature for Mari. She was able to make him happy, and that made _her_ happy. When she hugged him, or gave him a kiss goodnight, or just snuggled up on the couch and watched a movie with him, she felt… warm. Having someone around for her to love and take care of was… very comforting for the woman.

Yes, he was still _very_ much Yui's son, and she was _never_ going to forget that- but at the same time, he was also kind of... _her_ son.

.

It was nice, to say the least.

* * *

When Shinji was ten, Mari had decided to let him know what she'd pieced together about his mother's death. Before, she'd still talked about her to him, and shown him what photos she'd had- but by then, she'd felt that he was mature enough to deal with a heavier topic.

"Shinji," she'd started. "I want to talk to you about something."

The boy had looked up from his seat of the couch, curious.

"Yeah?"

Mari had strolled over, slowly, and sat herself down next to him.

"Now… this is going to be a pretty deep topic," she'd warned. "So, if _any_ of it makes you feel bad, you tell me right away, okay?"

"Mhm," he'd nodded, understanding it. Mari had nodded back.

"I… I wanted to tell you about your mom," she'd said. "How she died. Is that okay?"

"... Yes," he'd muttered. The woman looked away, focusing her eyes on something else.

"Yui… Yui was a brilliant scientist; I've told you that before," Mari said. "She and your father were part of a research group that was working with biotechnology and metaphysical biology- soul stuff, basically."

"They were conducting some sort of experiment, with something called 'Unit-01'. Your mom… your mom had decided to be the test subject. I don't know if she knew what was going to happen, or thought that is was an acceptable risk, or what- but I… I can't believe she'd let something like _that_ happen _on purpose_ , not when she had _you_." The woman took a break from talking, and rubbed the wetness from her eyes. Just describing it had been more painful for Mari than she'd anticipated. Still, she'd shouldered on.

"Whatever the case… it didn't work out right. Yui was… I don't know. Things went wrong, and now she's gone. All because of that… that _stupid experiment_ , and that da- stupid 'Unit-01' thing. That's all I know," she'd finished, slouching forwards. "I'm sorry. I had to tell you."

.

Beside her, Shinji had slumped into her side, pushing his body into hers. The air was still, solemn.

Tired.

She was tired, and emotional, and oh so glad that Shinji was there and hadn't made her stop talking because talking was the only way she could get it all _out_ of her, and-

.

-And Mari had stopped that train of thought there, and just laid back.

.

* * *

"Mom. Mom, wake up."

"Euh?" Mari grunted, eyes flickering open. Shinji sat up straight, a book folded up on his lap.

"What… what time is it?" the woman yawned, blinking the sleep out of her eyes.

"Um, the pilot said… about _three_ hours, until we land? Something like that," the boy answered, scratching the back of his head. "I mean, it _seemed_ like you'd gotten plenty of rest, so… yeah."

Mari furrowed her brow. There were three hours left, she'd gone to sleep _about_ an hour after take-off, and the flight was… yeah, roughly seven hours of sleep was good enough for her.

The woman shrugged to herself.

"...Yeah, I'm good, Shinji. But I hope you got some sleep _yourself_ , mister," Mari replied, giving him a casual, teasing smile.

"Yes, _mom_ ," the boy joked, adopting an exaggerated expression of exasperation. The two snickered, before Shinji trailed off and nodded. "No, but really; I _did_ get some rest. Eleven hours is a long time to be up when you're flying."

Mari reached over, and ruffled his hair.

"Good boy."

.

* * *

The rest of the way, things went well enough for them. After their flight landed, and the security check-through ended, the two stopped in the airport's food court to get a meal, and fully regain their bearings. It was still early in the morning, and the lack of flights- once Second Impact's damages had quieted down, air traffic had begun to drop- meant that the place was neither deafening, nor ridiculously overcrowded.

Of course, to be honest, it wasn't a very big meal- just a cup of ramen each. Even so, it was nice to have something to eat, and the low price certainly didn't hurt.

.

With that finished, it was off to the train station. Given Gendo's incredibly vague directions, Mari had been forced to _guess_ which stop to get off at, so she wasn't sure they'd gotten the right tickets. They were going to be _close_ at least- that much she knew. Now they stood at the station, waiting for the train to arrive.

"You know," Mari said. "This kind of reminds me of the last time I was here, back in 2005."

Shinji looked up, luggage sitting at his side. The woman smiled back down at him.

"Of course, this time we're both in a _far_ better state than we were then."

.

* * *

.

 _And now, an Author's Note:_

 _First off, I would like to apologise for the extreme delay in putting out this chapter. Yes, I know, it's a little short, unfortunately. I've_ _been having some troubles with the structure and content of the story- though I think I've now managed to work out some more of the kinks._

 _Additionally, my continued thanks to all the reviewers who sent their positivity! Your praise has certainly played a part in me being able to push myself to finish this recent section!_


	3. Hellfire

**_Evangelion: Illustrious Thesis_**

 _Chapter Three: Hellfire_

.

Deserted. Empty. The city seemed almost… lifeless. If there was one thing that neither of them had expected to see as they got off the train, it was _this_.

For a while, they waited at the edge of the station, sitting on one of the benches in the shade. The emptiness of the city was matched with its silence, the only noises those made by themselves or animals.

And then they heard it.

Speakers across station and city turned on, a static crackle droning for a few seconds, before an artificial voice spoke.

 _"_ _Your attention please, this is an urgent warning. As of 1230 hours today, a special state of emergency is being declared for the Tokai district as the epicentre. All residents should quickly and calmly evacuate to their designated shelters."_

Mari frowned. _That_ wasn't good.

 _"_ _We repeat- as of 12:30 today, a special state of emergency is being declared…"_

The woman stood up, and turned, looking around.

"Mom?"

"I heard," Mari said. "Shinji, I'm going to find a phone. Don't go anywhere." The boy nodded hurriedly, as Mari set off a little ways into the station. It wasn't hard to get ahold of one, as the phone booths were brightly coloured- but when Mari picked one up, all she heard on the other end was the same droning warning as that from the speakers.

 _~Damn,~_ the woman thought, hanging up. It'd be no use checking the other station phones- if this one was down, the others were almost certainly down as well. And with that 'special emergency', it wouldn't be a good idea to waste time trying again on the off chance that she was wrong.

Mari turned away, making her way back to the bench she'd left Shinji at. Thankfully, he'd stayed, much to her relief.

"Did you find one?" he asked. Mari shook her head.

"Phones are down. We're on our own."

The boy's face fell. Mari couldn't help but agree.

 _~No way of contact with the authorities, some mysterious emergency, unspecific directions from Gendo "I'm not going to explain anything" Rokubungi…_ wonderful,~ the woman thought. _~What_ disaster's _going to happen_ next _?~_

.

Unfortunately, it didn't take long for the answer to come. With the shriek of a rocket engine, a pair of missiles streaked overhead, fired at some unseen target.

"Missiles?!" Mari shouted. " _Here?!_ What for?!"

In the same horrifying way the last one had arrived, _this_ answer promptly appeared, rising above the buildings like a living mountain.

.

A _monster_.

* * *

At first, Mari could barely believe what she was seeing. The _thing_ \- a massive, barely humanoid shape, even taller than the buildings around it- had appeared almost in an instant, lumbering into view with an eerie, unreal silence. Even now, it moved with barely a sound, save for the crunch and thump of its footsteps.

Its appearance, too, seemed little like something from reality. The creature had the elongated proportions of a disjointed scarecrow, with stick-like limbs and a tapering torso, all covered in leathery, basil green flesh. Ash grey shell broke up the darkness, covering its shoulders and upper body with plates and spikes that curled around its chest like a ribcage. In the centre of these spikes, was some sort of orb, big and red- and above it, the face. The creature had no neck, and barely any head, but it did have a face. Made of the same pale shell as the rest of its plates, its visage was a simplified mask, with two black eye-holes, and a long, downwards-pointing beak.

Captivated by the unnaturalness of the thing, Mari and Shinji stared up at it- before another pair of missiles slammed into its side, detonating in a fiery roar. The air around the creature seemed to flicker, though the being itself showed no reaction. White-hot shrapnel showered the buildings around it, prompting Mari to grab Shinji and pull him back, retreating under the cover of the station's awning.

A UN Assault VTOL swooped into view on the other side, autocannon roaring. Glowing shells ricocheted off the being's mask, sparking like metal on impact. Once more, the monster did not seem the littlest bit harmed, taking another stride forwards with ease. This time, however, it responded.

A long, gangly arm rose up, tipped with three shiny black claws. The fingers spread apart, the palm aimed directly at the aircraft.

The orb in the centre of its chest began to glow.

Shinji spoke up.

"W-what's it do-"

The creature's hand flashed, and a beam of bright pink light lanced out, spearing the VTOL in an instant. A few seconds passed, the vehicle hanging skewered on the spike… before the fuel and explosives cooked off, and the VTOL burst apart in a ball of fire and wreckage. A chunk of an engine smashed into the station's stairs, shattering on impact.

As the creature retracted the spike into its arm, another pair of aircraft appeared, circling around cautiously. The assault craft trained their autocannons on it, ready to fire…

...and then they stopped, fronts angled towards the duo.

"What's going on? What happened?" Shinji asked.

"They must have seen us," Mari muttered.

* * *

"There's _what?!_ " the general demanded into the phone. Beside him, the other two glanced over, looks of concern on their faces.

 _"_ _Civilians, sir!"_ reported the pilot on the other end. _"Two of them; woman and child, down at the train station."_

The man grimaced.

"What are they _doing_ there? We sounded the alarm; everyone _should_ be in a shelter by now."

Another one of the three sighed.

"This Angel-thing's moving faster than we'd expected. Even with our preparations, it's barely been slowed down," he grumbled. "Not to mention that nothing's had any effect on it beyond provoking retaliation so far."

 _"_ _Sir, number three's shrapnel nearly hit them,"_ the pilot interrupted. _"If we keep shooting, there's a risk of collateral- be it ricochets or the target taking one of us down again. How do we respond?"_

The first general groaned. First the loss of the initial defense line, then the Angel's near-invulnerability, and now civilians to deal with. This was turning into a _disaster._

"General, if I may…" someone spoke up, their voice cold as the Arctic. The man scowled, and turned.

"What is it now, Ikari?"

Elevated behind them, a dark-haired man glared down, his eyes obscured by reflective amber spectacles.

"Bring the pilot's camera feed up on the main monitor. I need to confirm something," the man said.

"...fine."

The massive holographic screen blinked, switching its views to that of the pilot currently calling in. As he'd reported, there were two figures at the train station behind the Angel. Behind his glasses, the man narrowed his eyes, focusing.

The boy… brown hair, a slightly stringy body…

The woman… twin-tailed hairstyle, glasses...

.

"You will not open fire," Ikari stated. "To say nothing of how collateral would undoubtedly damage your reputation, generals, those two are _extremely_ important to Nerv. Should they come to harm from the actions of your forces…" The sentence wasn't finished, but the threat was clear- not to mention unnecessary, the general thought.

"Stand down," the man said into the transmitter, glaring at Ikari. "Do not continue the assault until the civilians are no longer within the line of fire."

His eyes narrowed.

"After that, give it hell!"

 _"_ _Yes, sir!"_

.

* * *

The VTOLs flew back, gaining more distance from the monster.

Then, between the whine of the jet engines, and the eerie silence of the creature, another sound caught the ears of Mari and Shinji; a car engine.

 _~A car? Who's driving at a time like this?~_ the former wondered- just before a bright blue, very beat-up looking Alpine Renault pulled up at the bottom of the station's stairs, and flung open its side doors.

"You two! Get in!"

 _~Who is this?~_ Mari thought- only to notice that Shinji had taken the opportunity. _~Oh,_ dammit!~

Not a few seconds after her godson took off, the brunette followed, racing down the steps and clamouring into the back seat as fast as she could. The doors were slammed shut, and the car's engine roared again.

As the vehicle sped off, Mari turned to look at their driver. The woman at the wheel was in her late twenties, with a head of black hair and a red and black uniform. She glanced towards them.

"Shinji Ikari? Mari Makinami?"

The two nodded, and the woman breathed a sigh of relief.

"Whew, good! Didn't accidentally pick up two complete strangers; that's a relief," she said, seemingly to herself, before looking back to the road.

"Um… sorry, but _who are you?_ " Shinji asked.

"Captain Misato Katsuragi," she answered, making a quick turn. "Nerv tactical director. Sorry about the wait- the Angel's arrival kinda screwed _everything_ up a little bit." As they roared down a road, the woman thumbed a button on the dashboard.

"HQ, this is Katsuragi. I've picked up the Third Child and his…" Misato paused, and glanced back at Mari.

"Godmother," the brunette finished.

"...godmother," Misato repeated. "We've left the immediate collateral zone; feel free to start shooting again. Katsuragi out." With that, the woman released her thumb hold on the button.

.

Shinji blinked.

"...Miss?"

"Yeah?"

"R-really; _who the hell are you?_ "


End file.
